RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes.
TAREAN (TAndem REpeat ANalyzer) is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.
The software package SiLiX (SIngle LInkage Clustering of Sequences) implements a new algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.
The Secator program for clustering protein sequences or coordinates data with the Secator rule on the dendrogram of hierarchical clustering.
The DPC program for clustering protein sequences or coordinates data with the DPC rule (small density between two high densities) for selecting the number of clusters